Abstract

LINE-1s (L1s) have contributed to gene structure variation and they can affect the expression of nearby genes in the human genome. Here, we collected 35 human-specific L1s that may play a role as alternative promoters. In addition, we identified 54 L1-chimeric transcripts generated from these L1s using bioinformatics’ tools and carried out reverse transcription-PCR to analyze their expressional pattern in 20 human normal tissues and 9 human cancer tissues. Consequently, 30 L1-chimeric transcripts were experimentally confirmed. Most L1-chimeric transcripts were broadly expressed. Interestingly, we found that EST CD709363 derived from C14orf37 gene was expressed in trachea only among normal tissues, but it was expressed in several cancer tissues including brain, lung, skin, and esophagus. We also newly identified three alternative transcripts, which were not in the UCSC genome database. One alternative transcript was derived from RABGAP1L gene and the other two transcripts were from CAMK4 gene. In addition, we analyzed putative transcription binding sites within the four L1s located in the promoter region. These had several transcription factor binding sites related to promoters. Our results show that human-specific L1s could contribute to human transcriptome diversity and transcriptional gene expression in different types of human tissues.

Electronic supplementary material

Supplementary material

Structural scheme of human-specific L1s (A) L1 had inserted into the human genome after the divergence of human and chimpanzee lineages and generated human-specific alternative transcripts by providing new promoters. (B) A full-length L1 contains untranslated regions (UTRs) at both side of two open reading frames (ORFs) and is about 6.9 kb in length. The 5′UTR of L1 provides bidirectional promoters, which can result in L1-chimeric transcripts (PPTX 42 kb).